[gmx-users] image centering
anoddlad at yahoo.com
Wed Dec 26 11:40:19 CET 2007
Have you tried running trjconv with -centre (selecting SOL, obviously), and then running trjconv -pbc on the result? I have a vague memory of finding seperating the commands gives a different result, as if the two options were interfering with each other. What does the output look like when you use the option -centre? If nothing else, seperating the commands might help you find the source of the problem.
----- Original Message ----
From: Myunggi Yi <myunggi at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, December 25, 2007 9:48:29 PM
Subject: [gmx-users] image centering
I have a membrane simulation trajectory,
in which the solvent (water and ions) is separated by lipid bilayer.
I want to center the solvent so that the membrane is separated by two layers at the bottom and top in the unit cell.
I have tried the followings.
trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -n ../memb.ndx -pbc cluster
trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -s ../Eq9/eq9.gro -n ../memb.ndx -center rect -pbc whole
Both pbc and center didn't work.
Is there any way to center the solvent?
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